Related papers: Unified perspective on proteins: A physics approac…
Understanding protein structure is of crucial importance in science, medicine and biotechnology. For about two decades, knowledge based potentials based on pairwise distances -- so-called "potentials of mean force" (PMFs) -- have been…
The process of protein synthesis in biological systems resembles a one dimensional driven lattice gas in which the particles have spatial extent, covering more than one lattice site. We expand the well studied Totally Asymmetric Exclusion…
Using the Helmholtz decomposition of the vector field of folding fluxes in a two-dimensional space of collective variables, a potential of the driving force for protein folding is introduced. The potential has two components. One component…
Context-dependent nature of biological phenomena are well documented in every branch of biology. While there have been few previous attempts to (implicitly) model various facets of biological context-dependence, a formal and general…
Studies of how protein fold have shown that the way protein clumps form in the test tube is similar to how proteins form the so-called ``amyloid'' deposits that are the pathological signal of a variety of diseases, among them the memory…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
Single molecule force spectroscopy provide details of the underlying energy surfaces of proteins which are essential to the understanding of their unfolding process. Recently, it has been observed experimentally that by pulling proteins in…
The ``unification'' of fundamental physical forces (interactions) imagines a ``single'' conceptual entity using which {\em all} the observable or physical phenomena, {\em ie}, changes to physical bodies, would be suitably describable. The…
I wish to expound a novel perspective of probing universal character of gravity. To begin with, inclusion of zero mass particle in mechanics leads to special relativity while its interaction with a universal force shared by all particles…
Protein folding is a phenomenon that has been studied for about 50 years and still remains as an unsolved problem. The main feature of this process is that it occurs as an all or none process, so a protein, can jump directly between folded…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
The prediction of the biologically active native conformation of a protein is one of the fundamental challenges of structural biology. This problem remains yet unsolved mainly due to three factors: the partial knowledge of the effective…
Entanglement and symmetrization lead to non-separable states that can modify physical properties. Using the example of atomic absorption we compare both types of effects when they are relevant at once. The presence of multi-particle…
Particle physics has evolved a coherent model that characterizes forces and particles at the most elementary level. This Standard Model, built from many theoretical and experimental studies, is in excellent accord with almost all current…
Self-assembly processes are widespread in nature, and lie at the heart of many biological and physical phenomena. The characteristics of self-assembly building blocks determine the structures that they form. Two crucial properties are the…
The theory of causal fermion systems is an approach to describe fundamental physics. Giving quantum mechanics, general relativity and quantum field theory as limiting cases, it is a candidate for a unified physical theory. We here give a…
In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…
The framework of generalized probabilistic theories is a powerful tool for studying the foundations of quantum physics. It provides the basis for a variety of recent findings that significantly improve our understanding of the rich physical…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
It is a fascinating subject to explore how well we can understand the processes of life on the basis of fundamental laws of physics. It is emphasised that viewing biological processes as manipulation of information extracts their essential…